/*
 * 
 *                This source code is part of
 * 
 *                 G   R   O   M   A   C   S
 * 
 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.0
 * 
 * Copyright (c) 1991-2001
 * BIOSON Research Institute, Dept. of Biophysical Chemistry
 * University of Groningen, The Netherlands
 * 
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 * 
 * If you want to redistribute modifications, please consider that
 * scientific software is very special. Version control is crucial -
 * bugs must be traceable. We will be happy to consider code for
 * inclusion in the official distribution, but derived work must not
 * be called official GROMACS. Details are found in the README & COPYING
 * files - if they are missing, get the official version at www.gromacs.org.
 * 
 * To help us fund GROMACS development, we humbly ask that you cite
 * the papers on the package - you can find them in the top README file.
 * 
 * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
 * 
 * And Hey:
 * Gyas ROwers Mature At Cryogenic Speed
 */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif



#include "statutil.h"
#include "typedefs.h"
#include "smalloc.h"
#include "vec.h"
#include "copyrite.h"
#include "statutil.h"
#include "tpxio.h"
#include "math.h"
#include "index.h"
#include "pbc.h"
#include "rmpbc.h"
#include "gmx_ana.h"


static const double bohr=0.529177249;  /* conversion factor to compensate for VMD plugin conversion... */

static void mequit(void){
  printf("Memory allocation error\n");
  exit(1);
}

int gmx_spatial(int argc,char *argv[])
{
  const char *desc[] = {
    "[TT]g_spatial[tt] calculates the spatial distribution function and ",
    "outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
    "This was developed from template.c (GROMACS-3.3). ",
    "For a system of 32K atoms and a 50ns trajectory, the SDF can be generated ",
    "in about 30 minutes, with most of the time dedicated to the two runs through ",
    "[TT]trjconv[tt] that are required to center everything properly. ",
    "This also takes a whole bunch of space (3 copies of the [TT].xtc[tt] file). ",
    "Still, the pictures are pretty and very informative when the fitted selection is properly made. ",
    "3-4 atoms in a widely mobile group like a free amino acid in solution works ",
    "well, or select the protein backbone in a stable folded structure to get the SDF ",
    "of solvent and look at the time-averaged solvation shell. ",
    "It is also possible using this program to generate the SDF based on some arbitrarty ",
    "Cartesian coordinate. To do that, simply omit the preliminary [TT]trjconv[tt] steps. \n",
    "USAGE: \n",
    "1. Use [TT]make_ndx[tt] to create a group containing the atoms around which you want the SDF \n",
    "2. [TT]trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none[tt] \n",
    "3. [TT]trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans[tt] \n",
    "4. run [TT]g_spatial[tt] on the [TT].xtc[tt] output of step #3. \n",
    "5. Load grid.cube into VMD and view as an isosurface. \n",
    "*** Systems such as micelles will require [TT]trjconv -pbc cluster[tt] between steps 1 and 2\n",
    "WARNINGS: \n",
    "The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
    "However, the preparatory [TT]-fit rot+trans[tt] option to [TT]trjconv[tt] implies that your system will be rotating ",
    "and translating in space (in order that the selected group does not). Therefore the values that are ",
    "returned will only be valid for some region around your central group/coordinate that has full overlap ",
    "with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
    "It is up to the user to ensure that this is the case. \n",
    "BUGS: \n",
    "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
    "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] ",
    "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
    "with an increased [TT]-nab[tt] value. \n",
    "RISKY OPTIONS: \n",
    "To reduce the amount of space and time required, you can output only the coords ",
    "that are going to be used in the first and subsequent run through [TT]trjconv[tt]. ",
    "However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since ",
    "memory is allocated for cube bins based on the initial coords and the [TT]-nab[tt] ",
    "(Number of Additional Bins) option value. \n"
  };
  
  static gmx_bool bPBC=FALSE;
  static gmx_bool bSHIFT=FALSE;
  static int iIGNOREOUTER=-1; /*Positive values may help if the surface is spikey */
  static gmx_bool bCUTDOWN=TRUE;
  static real rBINWIDTH=0.05; /* nm */
  static gmx_bool bCALCDIV=TRUE;
  static int iNAB=4;

  t_pargs pa[] = {
    { "-pbc",      FALSE, etBOOL, {&bPBC},
      "Use periodic boundary conditions for computing distances" },
    { "-div",      FALSE, etBOOL, {&bCALCDIV},
      "Calculate and apply the divisor for bin occupancies based on atoms/minimal cube size. Set as TRUE for visualization and as FALSE ([TT]-nodiv[tt]) to get accurate counts per frame" },
    { "-ign",      FALSE, etINT, {&iIGNOREOUTER},
      "Do not display this number of outer cubes (positive values may reduce boundary speckles; -1 ensures outer surface is visible)" },
    /*    { "-cut",      bCUTDOWN, etBOOL, {&bCUTDOWN},*/
    /*      "Display a total cube that is of minimal size" }, */
    { "-bin",      FALSE, etREAL, {&rBINWIDTH},
      "Width of the bins in nm" },
    { "-nab",      FALSE, etINT, {&iNAB},
      "Number of additional bins to ensure proper memory allocation" }
  };

  double MINBIN[3];
  double MAXBIN[3];
  t_topology top;
  int        ePBC;
  char       title[STRLEN];
  t_trxframe fr;
  rvec       *xtop,*shx[26];
  matrix     box,box_pbc;
  t_trxstatus *status;
  int        flags = TRX_READ_X;
  t_pbc      pbc;
  t_atoms    *atoms;
  int        natoms;
  char        *grpnm,*grpnmp;
  atom_id     *index,*indexp;
  int         i,nidx,nidxp;
  int v;
  int j,k;
  long ***bin=(long ***)NULL;
  long nbin[3];
  FILE *flp;
  long x,y,z,minx,miny,minz,maxx,maxy,maxz;
  long numfr, numcu;
  long tot,max,min;
  double norm;
  output_env_t oenv;
  gmx_rmpbc_t  gpbc=NULL;

  t_filenm fnm[] = {
    { efTPS,  NULL,  NULL, ffREAD },   /* this is for the topology */
    { efTRX, "-f", NULL, ffREAD },      /* and this for the trajectory */
    { efNDX, NULL, NULL, ffOPTRD }
  };
  
#define NFILE asize(fnm)

  CopyRight(stderr,argv[0]);

  /* This is the routine responsible for adding default options,
   * calling the X/motif interface, etc. */
  parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,
		    NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);

  read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,TRUE);
  sfree(xtop);

  atoms=&(top.atoms);
  printf("Select group to generate SDF:\n");
  get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidx,&index,&grpnm);
  printf("Select group to output coords (e.g. solute):\n");
  get_index(atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&nidxp,&indexp,&grpnmp);

  /* The first time we read data is a little special */
  natoms=read_first_frame(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&fr,flags);

  /* Memory Allocation */
  MINBIN[XX]=MAXBIN[XX]=fr.x[0][XX];
  MINBIN[YY]=MAXBIN[YY]=fr.x[0][YY];
  MINBIN[ZZ]=MAXBIN[ZZ]=fr.x[0][ZZ];
  for(i=1; i<top.atoms.nr; ++i) {
    if(fr.x[i][XX]<MINBIN[XX])MINBIN[XX]=fr.x[i][XX];
    if(fr.x[i][XX]>MAXBIN[XX])MAXBIN[XX]=fr.x[i][XX];
    if(fr.x[i][YY]<MINBIN[YY])MINBIN[YY]=fr.x[i][YY];
    if(fr.x[i][YY]>MAXBIN[YY])MAXBIN[YY]=fr.x[i][YY];
    if(fr.x[i][ZZ]<MINBIN[ZZ])MINBIN[ZZ]=fr.x[i][ZZ];
    if(fr.x[i][ZZ]>MAXBIN[ZZ])MAXBIN[ZZ]=fr.x[i][ZZ];
  }
  for (i=ZZ; i>=XX; --i){
    MAXBIN[i]=(ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH)+(double)iNAB)*rBINWIDTH+MINBIN[i];
    MINBIN[i]-=(double)iNAB*rBINWIDTH; 
    nbin[i]=(long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
  }
  bin=(long ***)malloc(nbin[XX]*sizeof(long **));
  if(!bin)mequit();
  for(i=0; i<nbin[XX]; ++i){
    bin[i]=(long **)malloc(nbin[YY]*sizeof(long *));
    if(!bin[i])mequit();
    for(j=0; j<nbin[YY]; ++j){
      bin[i][j]=(long *)calloc(nbin[ZZ],sizeof(long));
      if(!bin[i][j])mequit();
    }
  }
  copy_mat(box,box_pbc); 
  numfr=0;
  minx=miny=minz=999;
  maxx=maxy=maxz=0;

  if (bPBC)
    gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
  /* This is the main loop over frames */
  do {
    /* Must init pbc every step because of pressure coupling */

    copy_mat(box,box_pbc);
    if (bPBC) {
      gmx_rmpbc_trxfr(gpbc,&fr);
      set_pbc(&pbc,ePBC,box_pbc);
    }

    for(i=0; i<nidx; i++) {
      if(fr.x[index[i]][XX]<MINBIN[XX]||fr.x[index[i]][XX]>MAXBIN[XX]||
         fr.x[index[i]][YY]<MINBIN[YY]||fr.x[index[i]][YY]>MAXBIN[YY]||
         fr.x[index[i]][ZZ]<MINBIN[ZZ]||fr.x[index[i]][ZZ]>MAXBIN[ZZ])
	{
	  printf("There was an item outside of the allocated memory. Increase the value given with the -nab option.\n");
	  printf("Memory was allocated for [%f,%f,%f]\tto\t[%f,%f,%f]\n",MINBIN[XX],MINBIN[YY],MINBIN[ZZ],MAXBIN[XX],MAXBIN[YY],MAXBIN[ZZ]);
	  printf("Memory was required for [%f,%f,%f]\n",fr.x[index[i]][XX],fr.x[index[i]][YY],fr.x[index[i]][ZZ]);
	  exit(1);
	}
      x=(long)ceil((fr.x[index[i]][XX]-MINBIN[XX])/rBINWIDTH);
      y=(long)ceil((fr.x[index[i]][YY]-MINBIN[YY])/rBINWIDTH);
      z=(long)ceil((fr.x[index[i]][ZZ]-MINBIN[ZZ])/rBINWIDTH);
      ++bin[x][y][z];
      if(x<minx)minx=x;
      if(x>maxx)maxx=x;
      if(y<miny)miny=y;
      if(y>maxy)maxy=y;
      if(z<minz)minz=z;
      if(z>maxz)maxz=z;
    }
    numfr++;
    /* printf("%f\t%f\t%f\n",box[XX][XX],box[YY][YY],box[ZZ][ZZ]); */

  } while(read_next_frame(oenv,status,&fr));

  if (bPBC)
    gmx_rmpbc_done(gpbc);

  if(!bCUTDOWN){
    minx=miny=minz=0;
    maxx=nbin[XX];
    maxy=nbin[YY];
    maxz=nbin[ZZ];
  }

  /* OUTPUT */
  flp=ffopen("grid.cube","w");
  fprintf(flp,"Spatial Distribution Function\n");
  fprintf(flp,"test\n");
  fprintf(flp,"%5d%12.6f%12.6f%12.6f\n",nidxp,(MINBIN[XX]+(minx+iIGNOREOUTER)*rBINWIDTH)*10./bohr,(MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr,(MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr);
  fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxx-minx+1-(2*iIGNOREOUTER),rBINWIDTH*10./bohr,0.,0.);
  fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxy-miny+1-(2*iIGNOREOUTER),0.,rBINWIDTH*10./bohr,0.);
  fprintf(flp,"%5ld%12.6f%12.6f%12.6f\n",maxz-minz+1-(2*iIGNOREOUTER),0.,0.,rBINWIDTH*10./bohr);
  for(i=0; i<nidxp; i++){
    v=2;
    if(*(top.atoms.atomname[indexp[i]][0])=='C')v=6;
    if(*(top.atoms.atomname[indexp[i]][0])=='N')v=7;
    if(*(top.atoms.atomname[indexp[i]][0])=='O')v=8;
    if(*(top.atoms.atomname[indexp[i]][0])=='H')v=1;
    if(*(top.atoms.atomname[indexp[i]][0])=='S')v=16;
    fprintf(flp,"%5d%12.6f%12.6f%12.6f%12.6f\n",v,0.,(double)fr.x[indexp[i]][XX]*10./bohr,(double)fr.x[indexp[i]][YY]*10./bohr,(double)fr.x[indexp[i]][ZZ]*10./bohr);
  }

  tot=0;
  for(k=0;k<nbin[XX];k++) {
    if(!(k<minx||k>maxx))continue;
    for(j=0;j<nbin[YY];j++) {
      if(!(j<miny||j>maxy))continue;
      for(i=0;i<nbin[ZZ];i++) {
	if(!(i<minz||i>maxz))continue;
	if(bin[k][j][i]!=0){
	  printf("A bin was not empty when it should have been empty. Programming error.\n");
	  printf("bin[%d][%d][%d] was = %ld\n",k,j,i,bin[k][j][i]);
	  exit(1);
	}
      }
    }
  }

  min=999;
  max=0;
  for(k=0;k<nbin[XX];k++) {
    if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
    for(j=0;j<nbin[YY];j++) {
      if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
      for(i=0;i<nbin[ZZ];i++) {
	if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
	tot+=bin[k][j][i];
	if(bin[k][j][i]>max)max=bin[k][j][i];
	if(bin[k][j][i]<min)min=bin[k][j][i];
      }
    }
  }

  numcu=(maxx-minx+1-(2*iIGNOREOUTER))*(maxy-miny+1-(2*iIGNOREOUTER))*(maxz-minz+1-(2*iIGNOREOUTER));
  if(bCALCDIV){
    norm=((double)numcu*(double)numfr) / (double)tot;
  }else{
    norm=1.0;
  }

  for(k=0;k<nbin[XX];k++) {
    if(k<minx+iIGNOREOUTER||k>maxx-iIGNOREOUTER)continue;
    for(j=0;j<nbin[YY];j++) {
      if(j<miny+iIGNOREOUTER||j>maxy-iIGNOREOUTER)continue;
      for(i=0;i<nbin[ZZ];i++) {
	if(i<minz+iIGNOREOUTER||i>maxz-iIGNOREOUTER)continue;
	fprintf(flp,"%12.6f ",norm*(double)bin[k][j][i]/(double)numfr);
      }
      fprintf(flp,"\n");
    }
    fprintf(flp,"\n");
  }
  ffclose(flp);

  /* printf("x=%d to %d\n",minx,maxx); */
  /* printf("y=%d to %d\n",miny,maxy); */
  /* printf("z=%d to %d\n",minz,maxz); */

  if(bCALCDIV){
    printf("Counts per frame in all %ld cubes divided by %le\n",numcu,1.0/norm);
    printf("Normalized data: average %le, min %le, max %le\n",1.0,norm*(double)min/(double)numfr,norm*(double)max/(double)numfr);
  }else{
    printf("grid.cube contains counts per frame in all %ld cubes\n",numcu);
    printf("Raw data: average %le, min %le, max %le\n",1.0/norm,(double)min/(double)numfr,(double)max/(double)numfr);
  }

  thanx(stderr);
  
  return 0;
}

